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Pull requests: broadinstitute/gatk

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Pull requests list

Add keep-contig-names parameter
#8865 opened Jun 6, 2024 by gokalpcelik • Draft
3
Funcotator - removing the required transcript file
#8863 opened Jun 5, 2024 by jonn-smith • Draft
35
Rc vs 1365 hatcher testing parquet
#8845 opened May 23, 2024 by RoriCremer • Draft
Added long read walkers from long-running branch.
#8799 opened Apr 29, 2024 by jonn-smith Loading…
32
add echocallset as an option for integration test
#8757 opened Apr 1, 2024 by RoriCremer Loading…
DRAFT: Use temp snapshot of htsjdk with rans refactoring.
#8730 opened Mar 11, 2024 by cmnbroad • Draft
Test out the preview version of the next GKL (DO NOT MERGE)
#8712 opened Mar 4, 2024 by droazen Loading…
@jamesemery
16
Vs 299 spike speed up integration tests
#8706 opened Feb 29, 2024 by koncheto-broad • Draft
Remove hdfs support for GenomicsDB
#8698 opened Feb 16, 2024 by nalinigans • Draft
2
Refactoring a confusing method in GATKVariantContextUtils
#8690 opened Feb 13, 2024 by lbergelson • Draft
6
Adds option to write sample names in variantCounts
#8656 opened Jan 15, 2024 by odcambc • Draft
LearnReadOrientationModel loads tables for one ref context at a time, reducing memory demands 32x
#8639 opened Jan 4, 2024 by davidbenjamin Loading…
1
1
DRAGEN Joint Detection DO NOT MERGE
#8616 opened Dec 11, 2023 by davidbenjamin Loading…
2
test java 21
#8589 opened Nov 17, 2023 by lbergelson • Draft
1
Gg vs 887 streamline vat tsv extract
#8508 opened Aug 30, 2023 by gbggrant • Draft
10
Install the python-is-python3 package in our docker build
#8499 opened Aug 25, 2023 by droazen Loading…
1
@lbergelson
3
Update to gatk script to contain custom jdk path parameter
#8495 opened Aug 25, 2023 by gokalpcelik Loading…
8
Added percentage complete and expected time remaining to ProgressMeter
#8486 opened Aug 18, 2023 by jonn-smith Loading…
@droazen
5
The VariantFiltration docs said that you can specify that it should remove the filtered variants, which does not seem to be accurate
#8410 opened Jul 11, 2023 by KevinCLydon Loading…
setup_gcnvkernel.py: Add missing pyvcf dependency
#8341 opened May 24, 2023 by jmarshall Loading…
DRAFT: Changes for htsjdk VCFHeader refactoring
#8306 opened May 2, 2023 by cmnbroad • Draft
12
fix insufficient MaxProbPropagationDistance
#8294 opened Apr 24, 2023 by TomofumiSaka Loading…
fix wrong spanning deletion length with NON_REF of HaplotypeCaller
#8292 opened Apr 19, 2023 by TomofumiSaka Loading…
Experimental patch to ReferenceConfidenceVariantContextMerger for the GVS team
#8288 opened Apr 13, 2023 by droazen Loading…
4
fix for https://github.com/broadinstitute/gatk/issues/7304 ( haploid genotype and mendelian violations )
#8279 opened Apr 6, 2023 by lindenb Loading…
1
ProTip! What’s not been updated in a month: updated:<2025-12-06.